Monday, October 31, 2016

Evolution Evolves: Genetics, Natural Selection, and Epigenetics

Darwin’s indication of natural selection as a means of explaining the evolution of species has been successful at explaining much of what was known about life in his era.  He was apparently prescient enough to realize that there could be other mechanisms that might also play a role.  The growing recognition of epigenetics as a factor in evolution has created an extension of Darwin’s theory that has gained prominence in recent years.  Steven Rose presents a concise summary of these developments in an article in the London Review of Books with the curious title How to Get Another Thorax.

First, a definition is required.

“Phenotype is a Humpty-Dumptyish word, but can be roughly taken to mean any observable feature of a living organism, at any level from the molecular to the cellular to the entire organism and its behaviour. Richard Dawkins extended its definition by asserting that the dam a beaver builds is part of its phenotype.”

The term epigenetics in its current usage has been attributed to C. H. Waddington who coined it in the 1940s as a mechanism by which the attributes of a member of a given species might be modified by experiences during its development.  Waddington believed that these altered properties could, if reproduced over multiple generations, become incorporated as a heritable property of the species. 

“Epigenetics seeks to explain how, starting from an identical set of genes, the contingencies of development can lead to different outcomes.”

“He [Waddington] also went further, proposing that if a strongly canalised phenotypic change was repeated generation after generation, some random mutation would eventually catch up with it and it would be assimilated into the genome. He demonstrated that this was possible by exposing developing fruit fly embryos to ether, which induces them to develop a second thorax. After some twenty generations (it takes a fruit fly about seven days to develop from a fertilised egg to an adult ready to mate, so experiments using them are fast and easy), the flies developed the second thorax without exposure to the ether – the epigenetically induced bithorax had become fixed in the fly’s genome.”

Waddington was making these claims before knowledge of the structure of DNA and before modern techniques for genomic examination were available.  His ideas never caught on and faded from view for a time, only to return as research provided new insights.

The very fact that a single set of genes can produce an entire organism with many different types of cells indicates that there must be mechanisms that can turn genes on and off as needed to produce the cells with the various necessary functions.

“….the literary metaphor, universally employed by molecular biologists, isn’t accidental; they think of DNA as the language in which the Book of Life is written – in a scheduled flow during the development of the foetus, according to whether the cells are destined to become liver or brain, blood or bone. No gene works in isolation but as part of a collaboration. Many genes may be required to produce a single phenotype – more than fifty main gene variants have been shown to affect the chances that someone will contract coronary heart disease, for example – and a particular gene may influence many different phenotypic traits, depending on which organ’s cells it is active in. It is during this period of rapid growth that living organisms are at their most plastic, responding to environmental challenges by modifying anatomical, biochemical, physiological or behavioural phenotypic traits. This is epigenetic canalisation.”

The fact that environmental factors can alter genetic performance is obvious from studies of identical twins.  Beginning with the same genomes the pairs gradually drift apart in terms of health outcomes until eventually life expectancy becomes very poorly correlated.  This source provides relevant data.

“For molecular biologists, the task has been to discover the mechanisms by which external causes switch genes on and off. This has meant coming to terms with the significance of the fact that DNA is not a naked molecule but is protectively wrapped in a cling-film of proteins – histones – portions of which have to be peeled away before any particular length of DNA can be read; environmental factors affect the peeling process, and therefore the selection of genes to be read. A second important finding has been that during development segments of DNA become ‘marked’; a small molecular chunk, a methyl group (CH3), is attached to one of the DNA bases (generally C, cytosine). The presence of the methyl group prevents the DNA from being read – that is, it switches the gene off. Removing the methyl switches the gene on again. As the field of epigenetics develops, many more such mechanisms are likely to be discovered.”

“The environment in which a developing embryo is immersed is not unchanging; in mammals the hormonal status or diet of the pregnant female will affect the embryo and foetus, which responds adaptively to environmental challenges as methyl groups are added to or removed from specific regions of its DNA, thus controlling the direction of its development down one or another of the valleys in Waddington’s epigenetic landscape. What’s more, there is growing evidence that methyl marks placed on DNA during development persist and can be transferred to the next generation during reproduction, along with their phenotypic effects. Such transgenerational phenomena, though not their molecular mechanisms, have been known for decades, demonstrated experimentally in animals and observed in humans.”

As an example of an observation from the human population, Rose presents results from a wartime situation in which part of Holland was subjected to an imposed famine (referred to as the Rotterdam famine) while the remainder was not.

“During the winter of 1944 the retreating Germans imposed a blockade of food and fuel across western Holland, affecting some 4.5 million people. Children born to women who conceived or were pregnant during the famine period were found to be more susceptible to health problems such as diabetes, obesity and cardiovascular disease than their contemporaries born in the liberated eastern parts of the country. More surprising, at least to orthodox geneticists, is that similar susceptibilities have been found in their children and even their grandchildren.”

Such events are difficult to draw conclusions from because the descendents will intermarry with nonmembers of the particular population and any inherited tendencies due to the original event will be diluted.  But does that mean the effect has been erased?  Many traditional geneticists would like to believe so.

“A diminishing band of geneticists remain sceptical, arguing that unless transgenerational effects are constantly reinforced, they are gradually diluted and will eventually disappear, rather than being assimilated into the genome.”

“Epigeneticists respond with the bold claim that an epigenetic trait is, as one recent definition has it, a ‘stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence’.”

Those who consider themselves epigeneticists believe that genetics and development (nature and nurture) can no longer be considered independent fields.  Natural selection will still operate, but it must be within the context of an effectively unstable genetic basis, and it must consider environmental, social, and ecological conditions throughout the lifetime of the members of the species.  This approach is referred to as the Extended Evolutionary Synthesis (EES).

“The EES, which was presaged by Waddington, challenges the Neo-Darwinian picture of living creatures as ‘lumbering robots’, in Dawkins’s phrase, whose sole function, crushed as they are between the millstones of genes and environment, is to survive long enough to transmit the genes they carry to the next generation. Chickens, one might say, are merely an egg’s way of making more eggs.”

“In the EES, by contrast, selection operates not just on the individual adult organism but, through epigenetic processes, across the entire life cycle, and at multiple levels – genes, genomes, organisms, populations and even entire ecosystems. Co-operative interactions within and between species become important – not just competition. In the EES, as for the dialectical biologists of the 1930s, organisms do not merely accept the environment into which they are born, but work to seek out a more favourable one (the term for this is ‘niche construction’) and, having found it, they transform it, just as the beaver does by building a dam.”

The burgeoning science of epigenetics is spawning a number of research thrusts that could provide means of controlling diseases and affecting health outcomes.  Rose also warns us that it will also generate a number of commercial enterprises based on little or no science.

“Alongside the science, the pseudo-science proliferates. On the web, you can read articles claiming that mental effort can cause epigenetic change to ward off or induce cancer; advertisements sell vitamin supplements said to work through epigenetics. Practising epigeneticists try to police the boundary between science and myth while at the same time defending themselves against a residual genetic orthodoxy that continues to look on epigenetics with unease.”

One thing that should be clear to us as members of the human species is that we are not genetically and biologically inert.  Natural selection continues to work on us as we introduce new chemicals into our bodies, alter the food we eat, change our environment, vary the way we nurture our children, and even alter our mating patterns.  We are not who we were, and we are not who we will become.  And the changes may come much faster than we would have thought possible.

Sunday, October 23, 2016

Journalism: Objectivity, False Equivalence, and Extremism

The craziness of the current presidential campaign provides plenty of opportunities to ponder over the role of journalists in our society.  We know that there are any number of partisan sources of news and commentary on all sides of every issue, but we also would hope that there are media sources whose job it is to be objective and call a lie a lie and a fool a fool.  There seems to be little of this objectivity to be found in current reporting.  Why is that?

Journalists worry quite a bit about objectivity in their profession.  A wikipedia article tries to define what the term means.

“Journalistic objectivity is a significant principle of journalistic professionalism. Journalistic objectivity can refer to fairness, disinterestedness, factuality, and nonpartisanship, but most often encompasses all of these qualities.”

The listed attributes of journalistic objectivity are inconsistent with each other.  Can one be disinterested and factual at the same time?  In describing a political dispute, can one be factual and nonpartisan at the same time?  Factuality requires effort; the other three attributes do not.  The easy way out seems to be to skip the factuality and just report statements made by each side of an issue.  But if that is the practice, then of what value are journalists?

Shawn Otto addresses this issue from the perspective of reporting on science-related issues, but his thoughts are relevant to journalism in general.  His discussion is contained in his book The War on Science: Who's Waging It, Why It Matters, What We Can Do About It.

Otto begins by conveying a startling admission from a well-known journalist for one of the major networks.

“It should be noted that many journalists argue that their job is not to establish truth, but simply to relay information fairly.  This laissez-faire, hands-off view has come to dominate mainstream political journalism.  David Gregory, NBC News’s chief White House correspondent during the George W. Bush administration put it quite clearly in his defense of the White House press corps for not pushing President Bush on the lack of credible evidence of Saddam Hussein’s ‘weapons of mass destruction’ and the inconsistencies in Bush’s rationale for invasion before the United States entered Iraq.  ‘I think there are a lot of critics who think that….if we did not stand up and say this is bogus, and you’re a liar, and why are you doing this, that we didn’t do our job,’ said Gregory.  ‘I respectfully disagree.  It’s not our role.’”

Otto then respectfully asks whose role is it if not that of the press.

“How are the people to make well-informed decisions about momentous policies without accurate, reasonably objective information and a questioning of the powerful, asking for evidence?”

Journalists have long struggled with the issue of objectivity.  Often, they have been restricted by “journalistic conventions” as to what is considered standard and ethical practice.

“Journalism students are taught that every story is subjective, that it is impossible for a reporter to filter out their own biases, and that responsible reporters will acknowledge this.  In fact, they are told, to present a story as objective is fundamentally dishonest.  This notion is widespread.  Publications’ reporter guidelines contain it.  ‘There is no such thing as objectivity,’ the former NBC journalist Linda Ellerbee wrote.  ‘Any reporter who tells you he’s objective is lying to you.’  Students are taught that the best they can hope to achieve is to be fair and balanced.  The Society of Professional Journalists dropped ‘objectivity’ from its code of ethics in 1996.”

Otto, of course, disagrees with this mode of thinking.   

“Of course we are each subjective in our perspective, but there is such a thing as objectivity: a statement about reality that stands independent of our subjective qualities and is verifiable by others.  And such objectivity is attainable in reporting.  The belief in, and search for, objective truth might have motivated journalists such as David Gregory to have the confidence that it was ‘our role’ to push President Bush to produce evidence of the existence of weapons of mass destruction in Saddam Hussein’s Iraq before the United States invaded.  Is that a partisan position?  No.  Would it have been political?  Yes, and that is what responsible journalists do: they hold the powerful accountable.”

What we are left with is journalistic practice that is part intellectual cop out, part journalistic laziness, and part fear of offending any group that might result in a loss of revenue.  Political reporters think they need access to politicians.  They fear the loss of access if they give the politician a hard time.  It is too easy to just play nice and blame it on “accepted policy.”

“Very often, there is, in fact, objective knowledge that is readily available, and the misapplication of a reporter’s well-meaning view that there is no such thing as objectivity can become a recipe for disaster.  Cumulatively, this view becomes a danger to democracy, because it makes reporters vulnerable to easy manipulation by public-relations campaigns.  We are left with mainstream journalists (i.e., not those on talk radio or other purposely slanted news outlets) who often simply present ‘both sides’ of controversial issues, which gets us nowhere, doesn’t help the public make informed decisions, and plays into the hands of powerful vested interests.  Yet this has become the expectation and politicians become distrustful of journalists who don’t use such a he-said she-said approach.”

This refusal to seek objective truth can cause great damage.  This source cites an example indicating that the problem has existed for a long time.

“Another example of an objection to objectivity, according to communication scholar David Mindich, was the coverage that the major papers (most notably the New York Times) gave to the lynching of thousands of African Americans during the 1890s. News stories of the period often described with detachment the hanging, immolation and mutilation of people by mobs. Under the regimen of objectivity, news writers often attempted to balance these accounts by recounting the alleged transgressions of the victims that provoked the lynch mobs to fury. Mindich argues that this may have had the effect of normalizing the practice of lynching.”

Otto provides an example of the application of “balance and fairness” in the treatment of scientific issues.

“When a television news program presents a split screen with a scientist on one half representing the knowledge accumulated from tens of thousands of experiments performed by thousands of scientists, and then presents a charismatic advocate with an opposing opinion on the other half, as if the knowledge and opinion carry equal weight, this creates false balance.  It skews democracy towards extremes by giving equal weight to both opinion and knowledge.”

Otto’s reference to “false balance” has been more typically referred to as “false equivalence.”  Paul Krugman inveighs frequently against this journalistic practice.  Consider an example from his note The King of False Equivalence in which he disposes of the notion that Paul Ryan is a serious policy wonk with credible economic policies.

“….Ryan is not, repeat not, a serious, honest man of principle who has tainted his brand by supporting Donald Trump. He has been an obvious fraud all along, at least to anyone who can do budget arithmetic. His budget proposals invariably contain three elements:

1. Huge tax cuts for the wealthy.
2. Savage cuts in aid to the poor.
3. Mystery meat – claims that he will raise trillions by closing unspecified tax loopholes and save trillions cutting unspecified discretionary spending.”

“So how has he been able to get away with this? The main answer is that he has been a huge beneficiary of false balance. The media narrative requires that there be serious, principled policy wonks on both sides of the aisle; Ryan has become the designated symbol of that supposed equivalence, even though actual budget experts have torn his proposals to shreds on repeated occasions.”

Journalism’s attempt to be “fair” leads to the rendering equivalent of fact-based analyses with outrageous claims that are not based on facts.  This allows lies to be told and propagated indefinitely with the assistance of the imprimatur that derives from being sourced in mainstream media.

Otto concludes:

“….journalism becomes an implicit advocate for extreme views, weighting them and presenting them to the public as if they had equal merit with tested knowledge.  Journalism this fuels the extreme partisanship we see in public dialogue today, and feeds into the hands of the very power that journalists exist to challenge—vested interests who seek to circumvent evidence and undermine the democratic process to achieve a desired outcome.”

Sunday, October 2, 2016

Yet Another Contradiction Emerges In Market Capitalism: Investment Fund Management

It has become difficult to keep track of all the articles being written about market capitalism’s tendencies to work its way into some sort of calamity or dead end.  One of the latest involves the evolution of stock investment funds and their management.  An article by Charles Stein in Bloomberg Businessweek provides some necessary background.  The paper edition of the magazine used the title The Prof Who Made a Monkey of Wall Street.  For some reason, the online version was titled The Professor Who Was Right About Index Funds All Along

Stein introduces us to Burton Malkiel.

“In 1973, Malkiel, a Princeton professor, published the first version of his investment guide, A Random walk Down Wall Street. He wrote that “a blindfolded monkey throwing darts at the stock listings could select a portfolio that would do just as well as one selected by the experts.” Since most investors can’t beat the market average over time, he argued, they’d be better off in some kind of low-fee fund that simply held all of the stocks on a widely followed index. Problem was, no such retail fund existed.”

It took only a few years for Vangard to step in and create such an investment option.  Money managers were generally dubious at the time.

“….Ned Johnson, then the head of Fidelity Investments, spoke for most money managers when he told the Boston Globe, ‘I can’t believe that the great mass of investors are going to be satisfied with an ultimate goal of just achieving average returns’.”

Apparently, investors ultimately decided that “average” returns were better than casino type investing where the house’s take, money managers’ fees, insures the return is generally less than average.

“Things changed ... slowly, and then all at once. That first fund, the S&P 500-mimicking Vanguard 500 Index grew to a respectable $3 billion in assets in its first 20 years. But when it turned 40 years old on Aug. 31, it had more than $200 billion in assets, making it the third largest mutual fund, behind two other Vanguard index funds. From the end of 2007 through 2015—that is, since the financial crisis—domestic equity index funds saw a net inflow of investor money as active stockpickers grappled with outflows. About 34 percent of all fund assets are now in index trackers. Fidelity, though still a believer in the idea that managers can beat the markets, now advertises how inexpensive its own index funds are.”

As more money flows into index funds, a qualitative shift in desired investment outcomes occurs.  An “active” investor might feed money to a particular company in hopes that that firm will outdo all of its competitors, take away their business, and produce a dramatic increase in profit for itself.  Index funds, however, are “passive” investors.  They can charge low fees because they simply invest in the portfolio of companies that make up whatever index they are following.  This leads to a given fund having investments in many, if not all competitors in a given arena.  It is in the best interest of passive investors, therefore, for all companies to have stable, growing profits.  This is not the way capitalism is supposed to work.

The writer of the Free Exchange column in The Economist provided some thoughts on this issue in an article titled Stealth Socialism

“There is a contradiction at the heart of financial capitalism. The creative destruction that drives long-run growth depends on the picking of winners by bold, risk-taking capitalists. Yet the impressive (if not perfect) efficiency of markets means that trying to out-bet other investors is almost inevitably a losing proposition. Algorithmic punters trade away the tiniest of arbitrage opportunities near-instantaneously. Active investment strategies therefore amount to little more than a guessing game: one in which, over time, the losses from bad guesses eventually top the gains from good ones. Betting with the market—through broad index funds, for instance—is therefore a good way to maximise returns. Yet where does that leave capitalism, red in tooth and claw, and its need for bloody-minded nonconformists?”

“In America, since 2008, about $600 billion in holdings of actively managed mutual funds (which pick investments strategically) have been sold off, while $1 trillion has flowed into passive funds. So the passive funds now hold gargantuan ownership stakes in large, public firms. That makes for some awkward economics.”

“Research by Jan Fichtner, Eelke Heemskerk and Javier Garcia-Bernardo from the University of Amsterdam tracks the holdings of the “Big Three” asset managers: BlackRock, Vanguard and State Street. Treated as a single entity, they would now be the largest shareholder in just over 40% of listed American firms, which, adjusting for market capitalisation, account for nearly 80% of the market.”

If one believes that stock ownership provides at least the potential for determining corporate decisions, then these funds could have tremendous power over the national economy.  Such a level of influence by government would be considered socialism, thus the reference in the title.

“The revolution is here, but it was not the workers who seized ownership of the means of production; it was the asset managers.”

The author uses the airline industry to illustrate the danger of such a concentration of ownership by big investors.

“Institutional investors hold 77% of the shares of the companies providing services along the average airline route, for instance, and 44% of shares are controlled by just the top five investors. Adjusting measures of market concentration to take account of the control exercised by big asset managers suggests the industry is some ten times more concentrated than the level America’s Department of Justice considers indicative of market power. Fares are perhaps 3-5% higher than they would be if ownership of airlines were truly diffuse. In theory large asset-management firms might be quietly instructing the firms they own not to undercut rivals.”

If one is concerned by these developments, the options available are to limit investors’ access to the best mode of return on investment, or to limit major shareholders power to influence corporate decisions.  Neither of these is consistent with what market capitalism is supposed to be about.

The author holds out hope that the market will eventually recover on its own.

“Passive investment pays because active investors rush to price in new information. If passive investors took over the market entirely, unexploited opportunities would abound, active strategies would thrive and the passive-fund march would stall.”

However, it is best to hedge one’s confidence in the markets and consider some good-old-fashioned government intervention.

“As evidence of the side-effects of growth in passive funds accumulates, the best remedy might be for Washington to take its antitrust responsibilities more seriously.”

As for Malkiel, Stein tells us he still has money managers in his sights.

“Malkiel, 84, is now chief investment officer at Wealthfront, a Silicon Valley startup that’s become one of the leading robo-advisers—firms that use index funds to build automated investment plans for a fraction of the fees charged by traditional advisers. Just as index funds brought down the cost of investing, robo-advisers will bring down the cost of advice, says Malkiel, who spent 27 years on the Vanguard board. ‘The one thing I know is that the less I pay the purveyor, the more there will be left for me,’ he said.”

Capitalism isn’t what it was, nor is it yet what it will become.

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